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Proteomic Characterisation of the Salt Gland-Enriched Tissues of the Mangrove Tree Species Avicennia officinalis.

Tan WK, Lim TK, Loh CS, Kumar P, Lin Q - PLoS ONE (2015)

Bottom Line: This paper reports for the first time the proteomic analysis of salt gland-enriched tissues of a mangrove tree species.Information obtained from this study paves the way for future proteomic research aiming at elucidating the molecular mechanism underlying secretion in plant salt glands.The data have been deposited to the ProteomeXchange with identifier PXD000771.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, Singapore, 117543; NUS Environmental Research Institute, National University of Singapore, 5A Engineering Drive 1, T-Lab, #02-01, Singapore, Singapore, 117411.

ABSTRACT
Plant salt glands are nature's desalination devices that harbour potentially useful information pertaining to salt and water transport during secretion. As part of the program toward deciphering secretion mechanisms in salt glands, we used shotgun proteomics to compare the protein profiles of salt gland-enriched (isolated epidermal peels) and salt gland-deprived (mesophyll) tissues of the mangrove species Avicennia officinalis. The purpose of the work is to identify proteins that are present in the salt gland-enriched tissues. An average of 2189 and 977 proteins were identified from the epidermal peel and mesophyll tissues, respectively. Among these, 2188 proteins were identified in salt gland-enriched tissues and a total of 1032 selected proteins were categorized by Gene Ontology (GO) analysis. This paper reports for the first time the proteomic analysis of salt gland-enriched tissues of a mangrove tree species. Candidate proteins that may play a role in the desalination process of the mangrove salt glands and their potential localization were identified. Information obtained from this study paves the way for future proteomic research aiming at elucidating the molecular mechanism underlying secretion in plant salt glands. The data have been deposited to the ProteomeXchange with identifier PXD000771.

No MeSH data available.


Identification and analysis of salt gland-enriched proteome.(A) The experimental approach for generation of a salt gland-enriched proteome through the use of two distinct set of samples: total proteins from the adaxial (upper) epidermal peels (with salt glands) and from the mesophyll tissues (no salt glands). (B) The number of proteins that are identified in salt gland-enriched epidermal peels from three biological replicates is presented in the Venn diagram. Identified proteins from the salt gland-enriched tissues that were present in all the three biological replicates were grouped according to the number of unique peptides (C) and % sequence coverage (D). The identified proteins (D) were classified according to the protein’s sequence coverage.
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pone.0133386.g002: Identification and analysis of salt gland-enriched proteome.(A) The experimental approach for generation of a salt gland-enriched proteome through the use of two distinct set of samples: total proteins from the adaxial (upper) epidermal peels (with salt glands) and from the mesophyll tissues (no salt glands). (B) The number of proteins that are identified in salt gland-enriched epidermal peels from three biological replicates is presented in the Venn diagram. Identified proteins from the salt gland-enriched tissues that were present in all the three biological replicates were grouped according to the number of unique peptides (C) and % sequence coverage (D). The identified proteins (D) were classified according to the protein’s sequence coverage.

Mentions: The salt glands of Avicennia officinalis are microscopic (20–40 μm) structures found on the epidermal leaf surfaces (Fig 1A). They can secrete droplets of salt solutions, which appear circular in shape above the salt glands under a layer of oil when the adaxial (upper) epidermal peel (which harbours the salt glands) was viewed from the top (Fig 1B). These adaxial epidermal peels that are enriched with salt glands (Fig 1C) thus serve as good starting materials for the study of the salt gland proteome. To achieve this, proteins from both the adaxial epidermal peels (salt gland-enriched) and mesophyll tissues (salt gland-deprived) were extracted and compared (Fig 2A). For each extraction, approximately 2 mg proteins/g tissues and 9 mg proteins/g tissues were obtained from the epidermal peels and mesophyll tissues, respectively. A 2DLC/MS/MS analysis was performed on each of the trypsin-digested samples and identified proteins for each biological replicate were selected (< 1% FDR; S1–S6 Tables). An average of 2189 ± 128 (Table 1 and S1–S3 Tables) and 977 ± 150 (Table 1 and S4–S6 Tables) proteins were observed from the epidermal peels and mesophyll tissues, respectively. To obtain a list of proteins from salt gland-enriched tissues, only proteins that are found in epidermal peels but not in mesophyll tissues were considered. Data were sorted using nwCompare [23], with proteins found in any biological replicates for each tissue type taken into consideration and those extracted from epidermal peels and can be identified from mesophyll tissues eliminated. Using this approach, 2188 proteins are identified in salt gland-enriched tissues (Fig 2B and see S7 Table). Of these, 496 proteins were commonly found in all biological replicates, 536 proteins observed in two out of three biological replicates while remaining 1156 were present in one of the biological replicates (Fig 2B). Among the 496 proteins that were commonly found in all three biological replicates analysed, more than 25% of the proteins with at least one unique peptide was identified, while ~50% of the proteins with 2–5 unique peptides and the rest with at least 6 unique peptides identified (Fig 2C). By looking at the distribution of protein sequence coverage, more than 65% of the proteins identified showed a sequence coverage of 15–40% (Fig 2D).


Proteomic Characterisation of the Salt Gland-Enriched Tissues of the Mangrove Tree Species Avicennia officinalis.

Tan WK, Lim TK, Loh CS, Kumar P, Lin Q - PLoS ONE (2015)

Identification and analysis of salt gland-enriched proteome.(A) The experimental approach for generation of a salt gland-enriched proteome through the use of two distinct set of samples: total proteins from the adaxial (upper) epidermal peels (with salt glands) and from the mesophyll tissues (no salt glands). (B) The number of proteins that are identified in salt gland-enriched epidermal peels from three biological replicates is presented in the Venn diagram. Identified proteins from the salt gland-enriched tissues that were present in all the three biological replicates were grouped according to the number of unique peptides (C) and % sequence coverage (D). The identified proteins (D) were classified according to the protein’s sequence coverage.
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4508094&req=5

pone.0133386.g002: Identification and analysis of salt gland-enriched proteome.(A) The experimental approach for generation of a salt gland-enriched proteome through the use of two distinct set of samples: total proteins from the adaxial (upper) epidermal peels (with salt glands) and from the mesophyll tissues (no salt glands). (B) The number of proteins that are identified in salt gland-enriched epidermal peels from three biological replicates is presented in the Venn diagram. Identified proteins from the salt gland-enriched tissues that were present in all the three biological replicates were grouped according to the number of unique peptides (C) and % sequence coverage (D). The identified proteins (D) were classified according to the protein’s sequence coverage.
Mentions: The salt glands of Avicennia officinalis are microscopic (20–40 μm) structures found on the epidermal leaf surfaces (Fig 1A). They can secrete droplets of salt solutions, which appear circular in shape above the salt glands under a layer of oil when the adaxial (upper) epidermal peel (which harbours the salt glands) was viewed from the top (Fig 1B). These adaxial epidermal peels that are enriched with salt glands (Fig 1C) thus serve as good starting materials for the study of the salt gland proteome. To achieve this, proteins from both the adaxial epidermal peels (salt gland-enriched) and mesophyll tissues (salt gland-deprived) were extracted and compared (Fig 2A). For each extraction, approximately 2 mg proteins/g tissues and 9 mg proteins/g tissues were obtained from the epidermal peels and mesophyll tissues, respectively. A 2DLC/MS/MS analysis was performed on each of the trypsin-digested samples and identified proteins for each biological replicate were selected (< 1% FDR; S1–S6 Tables). An average of 2189 ± 128 (Table 1 and S1–S3 Tables) and 977 ± 150 (Table 1 and S4–S6 Tables) proteins were observed from the epidermal peels and mesophyll tissues, respectively. To obtain a list of proteins from salt gland-enriched tissues, only proteins that are found in epidermal peels but not in mesophyll tissues were considered. Data were sorted using nwCompare [23], with proteins found in any biological replicates for each tissue type taken into consideration and those extracted from epidermal peels and can be identified from mesophyll tissues eliminated. Using this approach, 2188 proteins are identified in salt gland-enriched tissues (Fig 2B and see S7 Table). Of these, 496 proteins were commonly found in all biological replicates, 536 proteins observed in two out of three biological replicates while remaining 1156 were present in one of the biological replicates (Fig 2B). Among the 496 proteins that were commonly found in all three biological replicates analysed, more than 25% of the proteins with at least one unique peptide was identified, while ~50% of the proteins with 2–5 unique peptides and the rest with at least 6 unique peptides identified (Fig 2C). By looking at the distribution of protein sequence coverage, more than 65% of the proteins identified showed a sequence coverage of 15–40% (Fig 2D).

Bottom Line: This paper reports for the first time the proteomic analysis of salt gland-enriched tissues of a mangrove tree species.Information obtained from this study paves the way for future proteomic research aiming at elucidating the molecular mechanism underlying secretion in plant salt glands.The data have been deposited to the ProteomeXchange with identifier PXD000771.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, Singapore, 117543; NUS Environmental Research Institute, National University of Singapore, 5A Engineering Drive 1, T-Lab, #02-01, Singapore, Singapore, 117411.

ABSTRACT
Plant salt glands are nature's desalination devices that harbour potentially useful information pertaining to salt and water transport during secretion. As part of the program toward deciphering secretion mechanisms in salt glands, we used shotgun proteomics to compare the protein profiles of salt gland-enriched (isolated epidermal peels) and salt gland-deprived (mesophyll) tissues of the mangrove species Avicennia officinalis. The purpose of the work is to identify proteins that are present in the salt gland-enriched tissues. An average of 2189 and 977 proteins were identified from the epidermal peel and mesophyll tissues, respectively. Among these, 2188 proteins were identified in salt gland-enriched tissues and a total of 1032 selected proteins were categorized by Gene Ontology (GO) analysis. This paper reports for the first time the proteomic analysis of salt gland-enriched tissues of a mangrove tree species. Candidate proteins that may play a role in the desalination process of the mangrove salt glands and their potential localization were identified. Information obtained from this study paves the way for future proteomic research aiming at elucidating the molecular mechanism underlying secretion in plant salt glands. The data have been deposited to the ProteomeXchange with identifier PXD000771.

No MeSH data available.